A protester burns a portrait of Syrian president Bashar al-Assad during a demonstration. Photograph: Bulent Kilic/AFP/Getty Images

Thousands of Syrians defied their government's bloody attempts to suppress protests, braving gunfire from security forces to demonstrate in Damascus and across the country.

At least 42 people were killed, most of them in the opposition stronghold of Deraa, where villagers tried to break through the security cordon to relieve its besieged population.

Further deaths were reported in Latakia and Homs after the security forces opened fire on demonstrators. There was news of protests in 50 towns and villages including Hama, Aleppo, the coastal cities of Latakia and Banias, Deir Ezzor in the east, and Qamishli in the north-east. Unrest was also reported on the Syria-Jordan border, which is straddled by the Haurani tribes.

Despite the government crackdown, the demonstrations, many starting as Friday worshippers left mosques, appeared to be at least as big as last week. Even more significantly, activists said, the protests spread closer to the centre of Damascus.

Demonstrators in the neighbourhoods of Barzeh, Midan, Bab Srejeh and Hajr al-Aswad faced security forces backed by soldiers for the first time.

Two witnesses in Midan told the Guardian that a crowd of 4,000 protesters who came out of Zain al-Abideen and Hassan mosques were dispersed by teargas and security forces with batons. "I counted 17 buses of security," said one, who asked not to be named.

Another said teargas and sound bombs were used, and the street to the main hospital was closed. He said shabiha (gangs connected to the ruling family) were terrorising the neighbourhood long after the demonstration was dispersed.

Meanwhile, the international community stepped up its pressure on Damascus. The UN human rights council in Geneva approved an investigation into the Syrian use of violence against protesters, and called for the immediate release of political prisoners and the lifting of restrictions on the press and the internet.

The US-drafted resolution passed despite the resistance of Russia, China and some Arab and African countries. However, it was watered down to omit mention of Syria's currently unopposed candidacy to join the council itself.

The UK envoy to the council, Peter Gooderham, said there could be "no impunity" for those who have committed human rights violations. "Those in power can see violations being committed in their name," he said. "They are accountable, too, for the violence and the deaths, even more so if they do nothing to stop these actions."

Last night, the US imposed sanctions on Syria's intelligence agency and two relatives of President Bashar al-Assad in Washington's first concrete steps in response to the crackdown.

Assad, Syria's long-serving ruler, was not among those targeted under an order signed by President Obama, but he could be named soon if violence by government forces against democracy protesters continued, a senior US official said.

"The sanctions that were announced today are intended to show the Syrian government that its behaviour and actions are going to be held to account," the US secretary of state, Hillary Clinton, told reporters.

Sanctions for alleged human rights abuses were imposed against Maher al-Assad, Bashar's brother, and Atif Najib, his cousin, together with Syria's General Intelligence Directorate and its chief.

EU officials also debated similar sanctions in Brussels, but these will not come into force until a ministerial meeting which may not take place for weeks.

Next month Damascus could come under pressure from another direction. Western diplomats say Yukiya Amano, director general of the UN's International Atomic Energy Agency, will state that Syria had been developing a nuclear reactor at a desert site bombed by Israel in 2007.

Syria has denied western allegations that the Dair Alzour site was intended to produce weapons-grade plutonium. Until now, the IAEA has sought more information before making a judgment, but has been blocked by the Syrian government.

If Amano declares Dair Alzour was in fact such a reactor, it could lead to Syria being referred to the UN security council for scrutiny of its nuclear ambitions.